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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AneuFinder_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AneuFinder’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
refineBreakpoints         130.065  1.680 136.737
simulateReads             105.641  4.495 114.629
heatmapAneuploidies       109.479  0.367 110.884
plotHeterogeneity          67.760  0.617  71.839
heatmapGenomewideClusters  60.619  0.333  61.434
correctGC                  53.046  2.655  59.049
karyotypeMeasures          54.686  0.562  57.634
heatmapGenomewide          52.169  0.388  53.106
annotateBreakpoints        30.807  0.807  33.812
getBreakpoints             26.711  0.846  28.447
consensusSegments          20.937  0.133  22.930
subsetByCNVprofile         13.247  0.077  14.107
getSCEcoordinates          11.377  0.492  12.237
findCNVs.strandseq          9.927  0.608  11.043
findCNVs                    8.803  0.746   9.650
variableWidthBins           9.358  0.155   9.963
loadFromFiles               9.164  0.248   9.853
clusterByQuality            6.137  0.154   7.123
blacklist                   4.201  0.205   5.293
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.